pMT06 was transfected into various cell types and mRNA barcode counts were sequenced together with pMT06 pDNA counts. In four different sequencing runs, data for all P53 & GR reporters was collected, and will be analyzed here.
Stuff learned from above figures:
Some samples can be excluded from further analysis because they don’t contain useful information, these samples are:
MCF7-KO-DMSO: rep2_seq1, rep1_seq1(?), r2_seq2(?), r1_seq3, r3_seq3
MCF7-KO-Nutlin: rep2_seq1, rep3_seq1(?), r1_seq2, r1_seq3, r3_seq3
MCF7-WT-DMSO: rep2_seq1, rep3_seq1
MCF7-WT-Nutlin: rep3_seq1, r2_seq2, r1_seq3
A549_DMSO: r2_seq3, r3_seq3
A549_Dex10: r2_seq3
A549_Dex100: r2_seq3
A549-Dex-1: r1_seq2, r2_seq3
mES-N2B27-HQ: rep1_seq1
mES-N2B27-RA: rep1_seq1, rep2_seq1
Divide cDNA barcode counts through pDNA barcode counts
paste("Run time: ",format(Sys.time()-StartTime))## [1] "Run time: 8.081767 mins"
getwd()## [1] "/DATA/usr/m.trauernicht/projects/SuRE_deep_scan_trp53_gr/analyses"
date()## [1] "Thu Jul 1 15:04:51 2021"
sessionInfo()## R version 4.0.5 (2021-03-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] tidyr_1.1.3 viridis_0.6.0 viridisLite_0.4.0
## [4] ggpointdensity_0.1.0 ggbiplot_0.55 scales_1.1.1
## [7] factoextra_1.0.7 shiny_1.6.0 pheatmap_1.0.12
## [10] gridExtra_2.3 RColorBrewer_1.1-2 readr_1.4.0
## [13] haven_2.4.1 ggbeeswarm_0.6.0 plotly_4.9.3
## [16] tibble_3.1.1 dplyr_1.0.5 vwr_0.3.0
## [19] latticeExtra_0.6-29 lattice_0.20-41 stringdist_0.9.6.3
## [22] GGally_2.1.1 ggpubr_0.4.0 ggplot2_3.3.3
## [25] stringr_1.4.0 plyr_1.8.6 data.table_1.14.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.2 tools_4.0.5 backports_1.2.1 bslib_0.2.4
## [5] utf8_1.2.1 R6_2.5.0 vipor_0.4.5 DBI_1.1.1
## [9] lazyeval_0.2.2 colorspace_2.0-0 withr_2.4.2 tidyselect_1.1.1
## [13] curl_4.3 compiler_4.0.5 labeling_0.4.2 sass_0.3.1
## [17] digest_0.6.27 foreign_0.8-81 rmarkdown_2.7 rio_0.5.26
## [21] jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.5.1.1 highr_0.9
## [25] fastmap_1.1.0 htmlwidgets_1.5.3 rlang_0.4.10 readxl_1.3.1
## [29] farver_2.1.0 jquerylib_0.1.4 generics_0.1.0 jsonlite_1.7.2
## [33] crosstalk_1.1.1 zip_2.1.1 car_3.0-10 magrittr_2.0.1
## [37] Rcpp_1.0.6 munsell_0.5.0 fansi_0.4.2 abind_1.4-5
## [41] lifecycle_1.0.0 stringi_1.5.3 yaml_2.2.1 carData_3.0-4
## [45] promises_1.2.0.1 ggrepel_0.9.1 forcats_0.5.1 crayon_1.4.1
## [49] hms_1.0.0 knitr_1.33 pillar_1.6.0 ggsignif_0.6.1
## [53] reshape2_1.4.4 glue_1.4.2 evaluate_0.14 png_0.1-7
## [57] vctrs_0.3.8 httpuv_1.6.0 cellranger_1.1.0 gtable_0.3.0
## [61] purrr_0.3.4 reshape_0.8.8 assertthat_0.2.1 xfun_0.22
## [65] openxlsx_4.2.3 mime_0.10 xtable_1.8-4 broom_0.7.6
## [69] rstatix_0.7.0 later_1.2.0 beeswarm_0.3.1 ellipsis_0.3.2